Analysis of the algorithm: From rankings to backup genes.
Ranking section
Table 1. Performance summary for every kernel and net before integration.
| Net | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| biological_process | ct | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | el | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | ka | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | rf | 1 | 1 | 1 | 1 | 0.904761904761905 |
| cellular_component | ct | 0.792672413793104 | 1 | 0.416666666666667 | 1 | 0.919354838709677 |
| cellular_component | el | 1 | 1 | 1 | 1 | 0.90625 |
| cellular_component | ka | 0.724137931034483 | 1 | 0.416666666666667 | 0.916666666666667 | 0.935483870967742 |
| cellular_component | rf | 0.724137931034483 | 1 | 0.414583333333335 | 1 | 0.926829268292683 |
| disease | ct | 0.363636363636364 | 1 | 0 | 1 | 0.956521739130435 |
| disease | el | 0.181818181818182 | 1 | 0 | 1 | 0.956521739130435 |
| disease | ka | 1 | 1 | 0.333333333333333 | 1 | 0.936170212765957 |
| disease | rf | 0.318181818181818 | 1 | 0 | 1 | 0.956521739130435 |
| gene_TF | ct | 1 | 1 | 0.6 | 1 | 0.918032786885246 |
| gene_TF | el | 1 | 1 | 1 | 1 | 0.918032786885246 |
| gene_TF | ka | 1 | 1 | 1 | 1 | 0.918032786885246 |
| gene_TF | node2vec | 0.427678571428572 | 1 | 0.4 | 1 | 0.933333333333333 |
| gene_TF | rf | 1 | 1 | 1 | 1 | 0.918032786885246 |
| gene_hgncGroup | ct | 0.407407407407407 | 1 | 0.666666666666667 | 1 | 0.905982905982906 |
| gene_hgncGroup | el | 1 | 1 | 1 | 1 | 0.9 |
| gene_hgncGroup | ka | 1 | 1 | 1 | 1 | 0.9 |
| gene_hgncGroup | rf | 1 | 1 | 1 | 1 | 0.9 |
| molecular_function | ct | 1 | 1 | 1 | 1 | 0.90625 |
| molecular_function | el | 1 | 1 | 0.916666666666667 | 1 | 0.90625 |
| molecular_function | ka | 1 | 1 | 1 | 1 | 0.90625 |
| molecular_function | rf | 1 | 1 | 1 | 1 | 0.90625 |
| pathway | ct | 0.288461538461538 | 1 | 0.272727272727273 | 1 | 0.91588785046729 |
| pathway | el | 1 | 1 | 1 | 1 | 0.904347826086957 |
| pathway | ka | 1 | 1 | 1 | 1 | 0.904347826086957 |
| pathway | node2vec | 1 | 1 | 1 | 1 | 0.904347826086957 |
| pathway | rf | 1 | 1 | 1 | 1 | 0.904347826086957 |
| phenotype | ct | 0.0434782608695652 | 1 | 0.166666666666667 | 1 | 0.92 |
| phenotype | el | 0.130434782608696 | 1 | 0.166666666666667 | 1 | 0.92 |
| phenotype | ka | 1 | 1 | 0.333333333333333 | 1 | 0.884615384615384 |
| phenotype | rf | 0.0434782608695652 | 1 | 0.166666666666667 | 1 | 0.92 |
| protein_interaction | ct | 1 | 1 | 1 | 1 | 0.909090909090909 |
| protein_interaction | el | 1 | 1 | 1 | 1 | 0.909090909090909 |
| protein_interaction | ka | 1 | 1 | 0.916666666666667 | 1 | 0.909090909090909 |
| protein_interaction | node2vec | 1 | 1 | 1 | 1 | 0.909090909090909 |
| protein_interaction | rf | 1 | 1 | 1 | 1 | 0.909090909090909 |
Table 2. Performance summary for every kernel after integration
| Integration | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| integration_mean_by_presence | ct | 1 | 1 | 1 | 1 | 0.909090909090909 |
| integration_mean_by_presence | el | 1 | 1 | 1 | 1 | 0.909090909090909 |
| integration_mean_by_presence | ka | 1 | 1 | 0.916666666666667 | 1 | 0.909090909090909 |
| integration_mean_by_presence | node2vec | 1 | 1 | 1 | 1 | 0.909090909090909 |
| integration_mean_by_presence | rf | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | ct | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | el | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | ka | 1 | 1 | 0.916666666666667 | 1 | 0.909090909090909 |
| mean | node2vec | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | rf | 1 | 1 | 1 | 1 | 0.909090909090909 |
ROC plots of non integrated kernels
ROC plots of integrated kernels
